Phoebe,
I know of no crystallography software which does this explicitly. The
new PHENIX B-factor restraints and to some extent TLS also do
indirectly use different restraints for surface exposed residues versus
buried side chains. In Phenix the sum over nearest neighbors within a
certain radius will reflect (see Pavel's previous email copied below),
to some extent, the packing environment of the residue. When using TLS,
residues on the outside of the protein will, in general, have larger
B-factors relative to those in the interior due to the rigid body
rotational motions of the protein.
Mark
Re: [ccp4bb]: Modelling disordered
side-chains / PHENIX B-factors
restraints
Date:
Wed, 10 Jan 2007 13:54:17 -0800
(15:54 CST)
B-factors restraints in PHENIX (if no TLS is used):
E_adp =
SUM_over_all_atoms( SUM_over_atoms_in_sphere_of_radius_R( [Bi-Bj]/[rij**n *
(Bi+Bj)**m] ) )
where rij is the distance between two atoms i and j, Bi and Bj -- their
B-factors, n and m are empirically found constants.
Cheers,
Pavel.
On Wed, 2007-01-10 at 18:46 -0600, [EMAIL PROTECTED] wrote:
> On a side note, it would be nice to have the restraints for side chain Bs
> dependent on location - e.g. surface side chains less restrained than buried.
>
> Does some program already do this and I haven't noticed?
>
> Phoebe
>
> At 03:19 PM 1/10/2007, Mark A. White wrote:
> >PS. The standard B-factor restraints are too tight, resulting in too
> >small a B-factor for most sidechains. I recommend increasing the sigma
> >values, using TLS, or Ian Tickle's variable restraints as implemented in
> >PMB/CNS (http://xray.utmb.edu/PMB). Also, PHENIX has a different method
> >of restraining B-factors which may be less prone to over-restraint. Peter
> >or Paul, do you have any information about this?
>
> ---------------------------------------------------------------------------------------------------------------------------
> Phoebe A. Rice
> Assoc. Prof., Dept. of Biochemistry & Molecular Biology
> The University of Chicago
> phone 773 834 1723
> fax 773 702 0439
> http://bmb.bsd.uchicago.edu/index.html
> http://www.nasa.gov/mission_pages/cassini/multimedia/pia06064.html
>
Sincerely yours,
Mark A. White, Ph.D.
Assistant Professor, Dept. Biochemistry and Molecular Biology,
Manager, Sealy Center for Structural Biology and Molecular Biophysics
X-ray Crystallography Laboratory,
Basic Science Building, Room 6.660 C
University of Texas Medical Branch
Galveston, TX 77555-0647
Tel. (409) 747-4747
Fax. (409) 747-4745
mailto://[EMAIL PROTECTED]
http://xray.utmb.edu
http://xray.utmb.edu/~white
